I don't think it will be long until someone puts all these together and demonstrates how the physiology of the gut more or less controls mental health for the most part.

Chinese medicine has done something (in my opinion) better that already for as long as 2000 yrs ago, at least.
The concept of "Shen" explains it: (the psychological Qi of organs and guts is managed by the heart not the brain.)[http://maciociaonline.blogspot.com/2012/11/shen-and-hun-psyche-in-chinese-medicine.html]
Therefore, in summary: trough Chinese herbology, among other practices they balance the qi of guts to achieve mental health.